8T95
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-(1,2,4,5)-IP4
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | 12% PEG8000, 100mM HEPES pH 7.0, 10mM NaH2PO4, 10% Ethylene Glycol, 5mM ADP and 10mM MgCl2, then soaked in 25% PEG8000, 100mM HEPES pH 7.0, 20% Ethylene Glycol with 5mM scyllo- (1,2,4,5)IP4, 5mM ADP and 10mM MgCl2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.83 | 56.6 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 64.258 | ¦Á = 90 |
b = 103.064 | ¦Â = 90 |
c = 104.065 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2021-11-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
1 | 2.6 | 50 | 99.9 | 0.091 | 0.095 | 0.026 | 1 | 9.6 | 13.2 | 10807 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.6 | 2.64 | 100 | 0.858 | 0.891 | 0.238 | 0.869 | 13.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 2.61 | 37.67 | 10209 | 552 | 99.33 | 0.17184 | 0.16871 | 0.22773 | RANDOM | 39.827 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.04 | 0.02 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.194 |
r_dihedral_angle_4_deg | 30.103 |
r_dihedral_angle_3_deg | 16.886 |
r_long_range_B_other | 9.656 |
r_long_range_B_refined | 9.649 |
r_dihedral_angle_1_deg | 7.781 |
r_scangle_other | 7.234 |
r_mcangle_other | 5.321 |
r_mcangle_it | 5.31 |
r_scbond_it | 4.734 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1764 |
Nucleic Acid Atoms | |
Solvent Atoms | 79 |
Heterogen Atoms | 56 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |
DENZO | data reduction |
PHASER | phasing |